Merge pull request #153 from KVSlab/fixate-deps

Fixate dependency versions

.github/workflows/check_and_test_package.yml

@@ -11,15 +11,15 @@ on:
  - cron: '0 8 * * *'
 
 env:
- CACHE_NUMBER: 11 # Increase to reset cache
+ CACHE_NUMBER: 12 # Increase to reset cache
 
 jobs:
  check-code:
  name: Check code
  runs-on: ubuntu-latest
 
  steps:
- - uses: actions/checkout@v4
+ - uses: actions/checkout@v3
  - uses: actions/setup-python@v5
  with:
  python-version: '3.8'
@@ -48,11 +48,13 @@ jobs:
  defaults:
  run: # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
  shell: bash -l {0}
+
  steps:
  - uses: actions/checkout@v3
  - uses: actions/setup-python@v5
  with:
  python-version: '3.8'
+
  - name: Setup and install with Mambaforge
  uses: conda-incubator/setup-miniconda@v2
  with:
@@ -63,19 +65,20 @@ jobs:
  use-mamba: true
  environment-file: environment-test.yml
  id: mamba
- - uses: actions/cache@v2
+
+ - uses: actions/cache@v3
  with:
  path: ${{ matrix.prefix }}
- key: ${{ matrix.label }}-${{ github.run_id }}-${{ env.CACHE_NUMBER }}
- restore-keys: ${{ matrix.label }}-
+ key: ${{ matrix.label }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment-test.yml') }}
+ restore-keys: ${{ matrix.label }}-${{ env.CACHE_NUMBER }}-
+
  - run: mamba env update -n vampy -f environment-test.yml
- if: steps.cache.outputs.cache-hit != 'true'
 
  - name: Install VaMPy
- run: python -m pip install .[test]
+ run: mamba run -n vampy python -m pip install '.[test]'
 
  - name: Run tests
- run: python -m pytest tests
+ run: mamba run -n vampy python -m pytest tests
 
  - name: Upload coverage report to Codecov
  if: matrix.os == 'ubuntu-latest'

.github/workflows/deploy_pages.yml

@@ -62,7 +62,7 @@ jobs:
  run: pip install -r requirements.txt
 
  - name: Install VaMPy
- run: python3 -m pip install .[test]
+ run: python3 -m pip install '.[test]'
 
  # Build the book
  - name: Build the book

environment-test.yml

@@ -6,13 +6,12 @@ channels:
 dependencies:
  - fenics
  - morphman
- - paramiko
- - pip
- - git
  - python >=3.8
- - expat==2.5 # Hotfix for https://gitlab.archlinux.org/archlinux/packaging/packages/paraview/-/issues/4
+ - pip==24.2
  - pip:
  - matplotlib
- - scipy
- - cppimport
+ - scipy==1.14.1
+ - numpy==1.24.4
+ - cppimport==22.8.2
+ - paramiko==3.4.1
  - git+https://github.com/KVSlab/OasisMove

environment.yml

@@ -6,12 +6,12 @@ channels:
 dependencies:
  - fenics
  - morphman
- - paramiko
- - pip
- - git
  - python >=3.8
- - expat==2.5 # Hotfix for https://gitlab.archlinux.org/archlinux/packaging/packages/paraview/-/issues/4
+ - pip==24.2
  - pip:
- - scipy
- - cppimport
+ - matplotlib
+ - scipy==1.14.1
+ - numpy==1.24.4
+ - cppimport==22.8.2
+ - paramiko==3.4.1
  - git+https://github.com/mikaem/Oasis

requirements.txt

@@ -1,8 +1,8 @@
 jupyter-book
-matplotlib
-numpy
 ghp-import
-cppimport
-scipy
 sphinx==5.3.0
 docutils==0.17.1
+matplotlib==3.9.2
+numpy==1.24.4
+cppimport==3.4.1
+scipy==1.14.1

src/vampy/automatedPostprocessing/compute_flow_and_simulation_metrics.py

@@ -334,6 +334,7 @@ def define_functions_and_iterate_dataset(time_to_average, dataset, dataset_avg,
  print("=" * 10, "Starting post processing", "=" * 10)
 
  counter = 0
+ tolerance = 1E-12
  for data, data_avg in zip(dataset, dataset_avg):
  counter += 1
 
@@ -402,14 +403,14 @@ def define_functions_and_iterate_dataset(time_to_average, dataset, dataset_avg,
 
  # Compute length scale
  t0 = Timer("Length scale")
- length_scale.vector().set_local((nu ** 3 / eps) ** (1. / 4))
+ length_scale.vector().set_local((nu ** 3 / (eps + tolerance)) ** (1. / 4))
  length_scale.vector().apply("insert")
  length_scale_cycle_avg.vector().axpy(1, length_scale.vector())
  t0.stop()
 
  # Compute time scale
  t0 = Timer("Time scale")
- time_scale.vector().set_local((nu / eps) ** 0.5)
+ time_scale.vector().set_local((nu / (eps + tolerance)) ** 0.5)
  time_scale.vector().apply("insert")
  time_scale_cycle_avg.vector().axpy(1, time_scale.vector())
  t0.stop()